Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,931,448	G→T	L265F (TTG→TTT)	rbsK →	ribokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,931,448	0	G	T	93.3%	99.3 / 0.4	30	L265F (TTG→TTT)	rbsK	ribokinase
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base T (14/14);  total (16/14)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

CAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAC  >  NZ_CP009273/3931365‑3931530                                                                                    |                                                                                   cAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGgaa                                                                              >  1:222628/1‑90 (MQ=255)          ccTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCa                                                                     <  1:289895/90‑1 (MQ=255)             ggATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTg                                                                  >  1:372436/1‑90 (MQ=255)                  ccGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTg                                                                                 <  2:44484/70‑1 (MQ=255)                  ccGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTg                                                                                 >  1:44484/1‑70 (MQ=255)                  ccGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCaga                                                             >  2:496442/1‑90 (MQ=255)                         cAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGAtt                                                      <  2:391753/90‑1 (MQ=255)                              tGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGttt                                                 >  1:598934/1‑90 (MQ=255)                                tCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTg                                               >  1:580455/1‑90 (MQ=255)                                        aTTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgct                                       <  2:600964/90‑1 (MQ=255)                                         ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                      >  1:451709/1‑90 (MQ=255)                                         ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                      >  1:215028/1‑90 (MQ=255)                                                   aaaTACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGAt                            <  1:162005/88‑1 (MQ=255)                                                    gaTACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGAtt                           <  2:36765/90‑1 (MQ=255)                                                     aTACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTg                          >  1:389275/1‑90 (MQ=255)                                                     aTACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTg                          >  1:12144/1‑90 (MQ=255)                                                          tttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTa                     <  1:552393/90‑1 (MQ=255)                                                             aaCGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAaca                  >  1:364582/1‑90 (MQ=255)                                                                 gTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTa              >  1:623612/1‑90 (MQ=255)                                                                  tGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaa             >  1:69456/1‑90 (MQ=255)                                                                  tGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaa             >  1:361080/1‑90 (MQ=255)                                                                  tGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaa             >  1:6876/1‑90 (MQ=255)                                                                   gCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaaa            <  2:32503/90‑1 (MQ=255)                                                                          tCACGGCATTTCTGGAAGAAAAACCATTGCTAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac     <  1:21445/90‑1 (MQ=255)                                                                          tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac     <  2:267158/90‑1 (MQ=255)                                                                          tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac     <  1:395024/90‑1 (MQ=255)                                                                            aCGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACaa   <  2:275855/90‑1 (MQ=255)                                                                            aCGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACaa   <  2:364582/90‑1 (MQ=255)                                                                            aCGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACaa   <  2:40293/90‑1 (MQ=255)                                                                             cGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAc  >  2:278716/1‑90 (MQ=255)                                                                                    |                                                                                   CAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAC  >  NZ_CP009273/3931365‑3931530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑